Here's my take...
Phase One: Uncanny X-Men film and future team characters introduction.
The Uncanny X-Men
I would want an MCU version of the X-Men to be more aligned with the comic history and aesthetic than we have previously gotten. I would establish mutancy as being a phenomenon that has been accelerating in recent years. Once the domain of the tin foil hat brigade, think reactionary Alex Jones paranoid conspiracy types, since the public battles of the various MCU heroes it's now out in the open, and as I said as a phenomenon it's growing. Teens are manifesting physical changes across a broad swath of demographics and it's an international story. I've never liked the idea of literally hundreds of millions of Mutants being out there. Spread across the globe I would rather it be more like between three to five million Mutants in the entirety of the world. Xavier, seeing the trends years ago, started his plan to integrate Mutants peacefully by taking in young Mutants in their early adolescence. Thus the team is mostly under 24 years old. And the team hasn't yet faced Magneto, for Xavier at this point thinks his old friend is dead.
The team, using a take on the classic blue and yellow uniforms which cover their faces to keep their identities secret, while being trained in their powers have mostly worked as a clandestine rescue operation. Finding young Mutants and bringing them back to the school. Sometimes this has put them at odds with everything from the legitimate authorities to violent Mutants beyond saving to average people filled with fear about a reality they cannot understand or embrace. After the public battle of the Avengers civil war, the revelation of the Inhumans, the rampages of the Hulk (and who knows... Maybe some manipulation by the Skrulls?) there are a lot in the public and government that are very wary of the growing Mutant population.
Enter the youngest and newest recruit of Xavier's school and team, Bobby Drake. Bobby will be the audience surrogate, learning about all this along with the viewer. Bobby has the double issue of being a mutant and being a young homosexual teen. He is brought in and we see how the X-Men are the oldest residents of the school... and they aren't that old to start with. Most of the other young Mutants are too young and too raw to ever send into the field to actually help rescue other Mutants, but Bobby has a better handle on what he can do than most his age, especially impressing field leader Scott Summers. It's apparent to him that Bobby can be useful.
I would intimate that Xavier has some kind of back channel to the government in some way, perhaps a picture of Xavier and a young Fury can be seen in his office. Touched on lightly in the Fox films (and just **** on by the constant retcons and bad writing that happened to the character post Claremont) Xavier to me would be a model of morality in action. Dedicated to bridging the divide he sees coming between the Mutants and humanity he is forced right now to keep his school and his strike force under the radar, and he knows the razor's edge he is dancing on. After all, a team of secret ID having Mutants that's appear out of nowhere to rescue others raises lots of legal and ethical questions. Xavier has a deep, if chaste relationship with geneticist and medical doctor Moira Mactagarrt, his "school's" physician.
Scott Summers, code named Cyclops, would be the truest of true believers. An orphan found by Xavier he's being groomed by the Prof. to be a leader and spokesman for Mutants. If you went into Scott's room at the mansion you would find a poster of the Evans Capt.. America on his wall. That is the type of person he wants to be. If anything, Scott, as a mutant that's experienced oppression and defamation, even after CIVIL WAR he's still a Cap fan. Can that make him a bit dorky to some? Sure. But he's never unsure of himself... Except around his teammate Jean.
Jean Grey, code named Marvel Girl, is the resident telekinetic and telepath on the team. Jean has great control over her telekinesis but is overwhelmed and unsure when it comes to her telepathy. She tries to remain a bit of a wallflower as other people's emotions assault her when they are very strong, and as a young beautiful woman she invokes a lot of emotions. This can even affect her telekinetic power. Jean feels like she has to maintain absolute focus all the time and it's draining to her on a daily basis. Scott actually admires this as no matter how hard he tries he cannot will his optic blast to cease without the aide of his visor. Jean is dedicated to the cause but deep down she wishes she could just get away from it all and do what she wants without any responsibility.
Warren Wortington III, code named Angel is the heir to a great fortune and is the team member with perhaps the most elitist view of things... And he hate s himself for it. Raised by blue bloods, since his wings sprouted he struggles with rectifying all he's been taught with the new reality that he is now, due to circumstances out of his control, one of the "undesirables" of society. And he knows that's an arrogant and above it all attitude. This internal battle makes him susceptible to arguments about the supposed superiority of mutant kind.
Hank McCoy, code named The Beast, is also a collection of internal struggles. Hank was already an overachiever, having graduated from high school after skipping quite a few grades in middle school. He was a savant, a fourteen year old college freshman when his mutancy manifested itself. He was already an outcast as a genius kid, picked on by bullies, and now he cannot even hide as a normal human being. Hank loves helping other Mutants, but personally, he wishes he wasn't one.
Xavier's team is forced to reveal themselves publicly when Charles is attacked while making an appearance on live TV talking about Mutants. Forced to reveal his power by what at first he believes to be anti-mutant militants it turns out it is actually the Brotherhood led by Magneto. Magneto hopes to make an example of his old friend, unaware of the team that Charles's has put together. Xavier is incapacitated and captured. As an example to all, Magneto declares Xavier a collaborator and traitor to mutant kind that he will execute right after he launches a devastating attack against the U.S. government and the world. Magneto does a lot of this under the guise of an anti-mutant group, so he is playing both sides in hopes of fomenting his "race War".
The team, back at the mansion are begged by Moira to go and help Charles, even though he has often told them that the team's secrecy needs to be inviolate. That is when an unexpected visitor shows up... Nick Fury. Fury lays out the relationship he and Xavier have had, both doing their best to keep a handle on the issues stemming from a rising mutant population. Fury believes Charles is too important to sacrifice, and he knows about the relationship between Magneto and Xavier, filling in the team. Fury knows Charles has asked them to keep themselves hidden but that time is over. Using his resources Fury gives them important info and Intel and then leaves the decision up to the team. They decide to go after Charles and this event, and the thwarting of Magneto and The Brotherhood, marks the full fledged public appearance of the X-Men.
And this appearance doesn't give the Mutants a PR victory. But that doesn't matter. Charles has hammerd into the team that they must do what is right, even in the face of bigotry and hate. Thus, now a known if mysterious presence in the world, the X-Men make their mark in the MCU. The first film I think needs to be kept tight, so the idea of including a sprawling cast of Mutants just to have them isn't in the cards in my mind. By the second film I would also find some way to organically have some, or all of the original five make a guest appearance in some other MCU film. Avengers movie, Spidey sequel, whatever. Just get the audience comfortable with this cast and invested in them and their relationships. So I would go at least two films concentrating on the original five and Xavier before bringing Logan, Kurt, Ororo, and Kitty into the fold and guest shots elsewhere to build up the first team's legacy.
Speaking of Wolverine and Storm...
Hulk Vs. Wolverine: Slash And Smash
Okay... were it up to me I would make the audience wait to see Logan with the team... But I wouldn't leave them completely without any Wolverine. So, however it plays out post A4, I would hope it ends with a Hulk/Banner still on the run and away from the Avengers. Taking a lot of cues from the animated short as well as his first appearance, this would be a film about Logan, a member of Canada's dept.H task force, Alpha Flight (name dropped but not shown) tracking, and attempting to eliminate Bruce Banner, aka, the Hulk. Taking place all across the wilds of Canada, it's a cat and mouse game between Banner and Logan and a third party, the mysterious Weapon X program. Weapon X wants Banner as a living juggernaut of destruction they hope they can control and replicate. Surprisingly Banner has been planning to use Weapon X methods in hopes of taming the Hulk. Logan, unsure of his past gets clues as to how he ended up the way he did tracking Banner/Hulk, who is searching for the various facilities that were used to make Logan who he is. Straight forward with lots of action this film would showcase a fan favorite in the Hulk, while introducing Logan before joining the X-Men. Rather than ending with a ROCKY III freeze frame I think both Banner (and Hulk) leave Logan with a grudging respect and maybe even a bond, as both are men struggling with monsters on the inside made all the worse by careless and cold applications of science. I would release this between Uncanny X-Men 1 and Uncanny X-Men 2, leaving Logan joining the team in the third film. Perhaps a post credit scene showing Logan is at least on the radar of Xavier.
As for Storm...
The King And The Goddess...
We cannot know exactly where Black Panther will be post A4 but we are all pretty young confident we are going to get a sequel. So I say introduce Ororo in there. Integrate her into the plot fully, hint at romantic tension, or have it be a simple cameo but make that connection. T'challa's history with her in this case doesn't have to totally mirror the comics but show that there is an attraction between the two, while also showing that her mutant status complicates their relationship. I am not saying you have to necessarily base the whole film around this (though... Why not?) but show the audience that Storm had a life before becoming a prominent X-Woman as it were. Hell, have Xavier cameo, giving T'challa a peak into her past, as well as establishing Charles and Storm's connection. At the end of said film Storm elects to stay in Africa, but not with T'challa in Wakanda. Sure, it's heart breaking but it leaves open the door for the couple to get together in the future. It's in the third X-Men film that Storm, paying her debt to Charles after he asks for her help, joins the team formally.
That's it in very broad strokes. Start with the first five in the blue and yellow, then showcase Logan and Storm away from the team first. As the story progresses break away from the secret strike team and make the team public super heroes, culminating in them wearing their individualized costumes. Keep the focus on a small cast though. When other characters leave they are replaced. And when they do leave it's not just some off screen deal (Looking at you FoX-Men 3 with your lack of Kurt...) it has some oomph to it. Frankly with them all home now I can get to see Hank leave the X-Men and take up residence with the Avengers.
Look I get everyone has favorites that they want to see, but as the sprawling casts of the Fox films show none are particularly well served by simply having blink and you'll miss them cameos or being background characters with no dialog. Focus on the heroic characters is the MCU way, and that gets diluted when you decide every mutant that ever appeared needs to show up. So... Start small and then build. This will ensure quality and that's all any of us wants from an MCU X-MEN product.
